From: mohammad goodarzi (mo.goodarzi82_at_gmail.com)
Date: Wed Dec 11 2019 - 11:22:15 CST
Hello,
I used CGENFF for it. when I import the molecule parameters it gives error
like error on the first line
LIGPARGEN GENERATED GRO FILE
12
1BNZ C00 1 -3.378 0.507 0.291
1BNZ C01 2 -3.455 0.482 0.404
1BNZ C02 3 -3.297 0.620 0.288
1BNZ H03 4 -3.381 0.439 0.207
1BNZ C04 5 -3.453 0.568 0.514
1BNZ H05 6 -3.518 0.395 0.406
1BNZ C06 7 -3.371 0.680 0.512
1BNZ H07 8 -3.515 0.548 0.601
1BNZ C08 9 -3.296 0.705 0.397
1BNZ H09 10 -3.366 0.747 0.596
1BNZ H0A 11 -3.234 0.793 0.394
1BNZ H0B 12 -3.235 0.641 0.202
1.00000 1.00000 1.00000
then I remove the first line and it give error on BNZ.
how should the parameter file look like?
Thanks
Mo
On Wed, Dec 11, 2019 at 1:51 AM Adupa Vasista <adupavasista_at_gmail.com>
wrote:
> Use CGENFF to get parameters.
>
> Thank You.
>
> On Tue, Dec 10, 2019 at 11:45 PM mohammad goodarzi <
> mo.goodarzi82_at_gmail.com> wrote:
>
>> Adupa,
>>
>> Yes the attached molecule is there too, can you please tell me how to
>> make the parameter for it?
>>
>> Thanks a lot
>>
>> On Tue, Dec 10, 2019 at 11:28 AM Adupa Vasista <adupavasista_at_gmail.com>
>> wrote:
>>
>>> Are there any other molecules other than protein? If so, then you have
>>> to add the parameters for that molecule too.
>>>
>>> and while using CHARMM36, better add carb.prm separately instead of
>>> lipid_prot_carb.prm
>>>
>>> On Tue, Dec 10, 2019 at 10:36 PM mohammad goodarzi <
>>> mo.goodarzi82_at_gmail.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> I have read a number of posts but none answered me this question.
>>>> I am getting error as
>>>>
>>>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>>>
>>>> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N287
>>>>
>>>>
>>>> Charm++ fatal error:
>>>>
>>>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N287
>>>>
>>>>
>>>> Abort trap: 6
>>>>
>>>>
>>>> and my parameters are
>>>>
>>>> # Force-Field Parameters
>>>> paraTypeCharmm on
>>>> parameters ./par_all36_lipid_prot_carb.prm
>>>> parameters ./par_all36_lipid.prm
>>>> parameters ./par_all36_prot.prm
>>>> parameters ./par_all36_na.prm
>>>>
>>>>
>>>> I just don't know what to add more, whatever I add or remove I get the
>>>> same error
>>>>
>>>> Thanks
>>>> Mo
>>>>
>>>
>>>
>>> --
>>>
>>> *A.VasistaM.Tech,Department Of Chemical Engineering,*
>>> *IIT Guwahati.*
>>>
>>
>
> --
>
> *A.VasistaM.Tech,Department Of Chemical Engineering,*
> *IIT Guwahati.*
>
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